If you go the Partition Magic route, which includes their Boot Magic boot programme, you should ideally re-nstall it after each OS has been loaded.

Why are you still messing around with Win9X anyway? My guess is that when you're set up so that the partition or HD with W2X can see the one with Win98, that's when your problems will really begin. Getting Win9X to sit comfortably alongside other OSs, especially other Windows OSs, can be serious hassle.